Add doxygen for high level modules. (#1839)

* Add doxygen for high level modules.

* Committing clang-format changes

* Correct spelling based on spelling check.

* Committing clang-format changes

Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

7 files changed, 1134 insertions, 8 deletions

diff --git a/doxygen/dox/ReferenceManual.dox b/doxygen/dox/ReferenceManual.dox
index c477813..bc5a544 100644
--- a/doxygen/dox/ReferenceManual.dox
+++ b/doxygen/dox/ReferenceManual.dox
@@ -33,19 +33,26 @@ The functions provided by the HDF5 C-API are grouped into the following
 \li Functions with \ref ASYNC "asynchronous variants"
 \li \ref api-compat-macros
 \li <a href="./deprecated.html">Deprecated functions</a>
-\li High-level Extensions
+\li \ref high_level
     <ul>
-    <li><a href="https://portal.hdfgroup.org/display/HDF5/Lite">\Bold{HDF5 Lite} (H5LT)</a></li>
-    <li><a href="https://portal.hdfgroup.org/display/HDF5/Images">\Bold{HDF5 Image} (H5IM)</a></li>
-    <li><a href="https://portal.hdfgroup.org/display/HDF5/Tables">\Bold{HDF5 Table} (H5TB)</a></li>
-    <li><a href="https://portal.hdfgroup.org/display/HDF5/Packet+Tables">\Bold{HDF5 Packet Table} (H5TB)</a></li>
-    <li><a href="https://portal.hdfgroup.org/display/HDF5/Dimension+Scales">\Bold{HDF5 Dimension Scale} (H5DS)</a></li>
+    <li>\ref H5LT "Lite (H5LT, H5LD)"
+    <li>\ref H5IM "Images (H5IM)"
+    <li>\ref H5TB "Table (H5TB)"
+    <li>\ref H5PT "Packet Table (H5PT)"
+    <li>\ref H5DS "Dimension Scale (H5DS)"
+    <li>\ref H5DO "Optimizations (H5DO)"
+    <li>\ref H5LR "Extensions (H5LR, H5LT)"
     </ul>
 </td></tr>
 <tr><td colspan="3" style="border: none;">
-\ref H5 \ref H5A \ref H5D \ref H5E \ref H5ES \ref H5F \ref H5G \ref H5I \ref H5L
+\a Core \a library: \ref H5 \ref H5A \ref H5D \ref H5E \ref H5ES \ref H5F \ref H5G \ref H5I \ref H5L
 \ref H5M \ref H5O \ref H5P \ref H5PL \ref H5R \ref H5S \ref H5T \ref H5VL \ref H5Z
 </td></tr>
+
+<tr><td colspan="3" style="border: none;">
+\a High-level \a library: \ref H5LT \ref H5IM \ref H5TB \ref H5PT \ref H5DS \ref H5DO \ref H5LR
+</td></tr>
+
 </table>
 
 </td></tr>
@@ -86,4 +93,4 @@ Break a leg!
      <a href="https://github.com/HDFGroup/hdf5/pulls">pull request</a> !\n
      See the \ref RMT for general guidance.
 
-*/
\ No newline at end of file
+*/
diff --git a/doxygen/dox/high_level/extension.dox b/doxygen/dox/high_level/extension.dox
new file mode 100644
index 0000000..1481bdd
--- /dev/null
+++ b/doxygen/dox/high_level/extension.dox
@@ -0,0 +1,657 @@
+/** \defgroup H5LR Extensions
+ *
+ * <em>Working with region references, hyperslab selections, 
+ * and bit-fields (H5LR, H5LT)</em>
+ *
+ * The following reference manual entries describe high-level HDF5 C and Fortran APIs 
+ * for working with region references, hyperslab selections, and bit-fields. 
+ * These functions were created as part of a project supporting 
+ * NPP/NPOESS Data Production and Exploitation (
+ * <a href="https://support.hdfgroup.org/projects/jpss/documentation">
+ * project </a>, 
+ * <a href="https://gamma.hdfgroup.org/ftp/pub/outgoing/NPOESS/source">
+ * software </a>). 
+ * While they were written to facilitate access to NPP, NPOESS, and JPSS 
+ * data in the HDF5 format, these functions may be useful to anyone working 
+ * with region references, hyperslab selections, or bit-fields.
+ *
+ * Note that these functions are not part of the standard HDF5 distribution; 
+ * the 
+ * <a href="https://gamma.hdfgroup.org/ftp/pub/outgoing/NPOESS/source">
+ * software </a> 
+ * must be separately downloaded and installed.
+ *
+ * A comprehensive guide to this library, 
+ * <a href="https://support.hdfgroup.org/projects/jpss/documentation/HL/UG/NPOESS_HL-UG.pdf"> 
+ * <em>User Guide to the HDF5 High-level Library for Handling Region References and Hyperslab Selections</em></a>
+ * is available at 
+ * https://support.hdfgroup.org/projects/jpss/documentation/HL/UG/NPOESS_HL-UG.pdf.
+ *
+ * - \ref H5LRcopy_reference
+ *        \n Copies data from the specified dataset to a new location and 
+ *        creates a reference to it.
+ * - \ref H5LRcopy_region
+ *        \n  Copies data from a referenced region to a region in a 
+ *        destination dataset.
+ * - \ref H5LRcreate_ref_to_all
+ *        \n  Creates a dataset with the region references to the data in all 
+ *        datasets located under a specified group in a file or creates a 
+ *        dataset with object references to all objects (groups or datasets) 
+ *        located under a specified group in a file.
+ * - \ref H5LRcreate_region_references
+ *        \n Creates an array of region references using an array of paths to 
+ *        datasets and an array of corresponding hyperslab descriptions.
+ * - \ref H5LRget_region_info
+ *        \n Retrieves information about the data a region reference points to.
+ * - \ref H5LRmake_dataset
+ *        \n Creates and writes a dataset containing a list of 
+ *        region references.
+ * - \ref H5LRread_region
+ *        \n  Retrieves raw data pointed to by a region reference to 
+ *        an application buffer.
+ * - \ref H5LTcopy_region
+ *        \n Copies data from a specified region in a source dataset 
+ *        to a specified region in a destination dataset.
+ * - \ref H5LTread_bitfield_value
+ *        \n Retrieves the values of quality flags for each element 
+ *        to the application provided buffer.
+ * - \ref H5LTread_region
+ *        \n Reads selected data to an application buffer.
+ * .
+ */
+
+/*-------------------------------------------------------------------------
+ *
+ * Make dataset functions
+ *
+ *-------------------------------------------------------------------------
+ */
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5LR
+ *
+ * \brief Creates and writes a dataset containing a list of region references.
+ *
+ * \fgdta_loc_id
+ * \param[in] path          Path to the dataset being created
+ * \param[in] type_id       Datatype of the dataset
+ * \param[in] buf_size      Size of the \p loc_id_ref and \p buf arrays
+ * \param[in] loc_id_ref    Array of object identifiers; each identifier 
+ *                          describes to which HDF5 file the corresponding 
+ *                          region reference belongs to
+ * \param[in] buf           Array of region references
+ *
+ * \return \herr_t
+ *
+ * \details Given an array of size \p buf_size of region references \p buf, 
+ *          the function will create a dataset with path \p path, at location 
+ *          specified by \p loc_id and of a datatype specified by \p type_id, 
+ *          and will write data associated with each region reference in the order 
+ *          corresponding to the order of the region references in the buffer. 
+ *          It is assumed that all referenced hyperslabs have the same dimensionality, 
+ *          and only the size of the slowest changing dimension may differ. 
+ *          Each reference in the \p buf array belongs to the file identified 
+ *          by the corresponding object identifiers in the array \p loc_id_ref.
+ *
+ *          If \p path does not exist in \p loc_id then the function will 
+ *          create the path specified by \p path automatically.
+ *
+ * \version 1.1 Fortran wrapper introduced in this release.
+ *
+ * \since 1.0
+ *
+ */
+H5_HLRDLL herr_t H5LRmake_dataset(hid_t loc_id,
+				 const char *path, 
+				 hid_t type_id, const size_t buf_size,
+				 const hid_t *loc_id_ref,
+				 const hdset_reg_ref_t *buf);
+
+/*-------------------------------------------------------------------------
+ *
+ * Make and manipulate dataset region references functions
+ *
+ *-------------------------------------------------------------------------
+ */
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5LR
+ *
+ * \brief Creates an array of region references using an array of paths to 
+ *        datasets and an array of corresponding hyperslab descriptions.
+ *
+ * \param[in] obj_id        File identifier for the HDF5 file containing
+ *                          the referenced regions or an object identifier
+ *                          for any object in that file
+ * \param[in] num_elem      Number of elements in the \p path and 
+ *                          \p buf arrays
+ * \param[in] path          Array of pointers to strings, which contain 
+ *                          the paths to the target datasets for the 
+ *                          region references
+ * \param[in] block_coord   Array of hyperslab coordinate
+ * \param[out] buf          Buffer for returning an array of region 
+ *                          references
+ *
+ * \return \herr_t
+ *
+ * \note    **Motivation:**
+ * \note    H5LRcreate_region_references() is useful when creating 
+ *          large numbers of similar region references.
+ *
+ * \details H5LRcreate_region_references() creates a list of region references 
+ *          given an array of paths to datasets and another array listing the 
+ *          corner coordinates of the corresponding hyperslabs.
+ *
+ *          \p path parameter is an array of pointers to strings.
+ *
+ *          \p num_elem specifies the number of region references to be created, 
+ *          thus specifying the size of the \p path and \p _buf arrays.
+ *
+ *          Buffer \p block_coord has size 2*rank and is the coordinates of the 
+ *          starting point following by the coordinates of the ending point of 
+ *          the hyperslab, repeated \p num_elem times for each hyperslab. 
+ *          For example, creating two region references to two hyperslabs, 
+ *          one with a rectangular hyperslab region starting at element (2,2) 
+ *          to element (5,4) and the second rectangular region starting at 
+ *          element (7,7) to element (9,10), results in \p block_coord 
+ *          being {2,2,5,4, 7,7,9,10}.
+ *
+ *          The rank of the hyperslab will be the same as the rank of the 
+ *          target dataset. H5LRcreate_region_references() will retrieve 
+ *          the rank for each dataset and will use those values to interpret 
+ *          the values in the buffer. Please note that rank may vary from one 
+ *          dataset to another.
+ *
+ * \version 1.1 Fortran wrapper introduced in this release.
+ *
+ * \since 1.0
+ *
+ */
+H5_HLRDLL herr_t H5LRcreate_region_references(hid_t obj_id,
+					     size_t num_elem,
+					     const char **path,
+					     const hsize_t *block_coord,
+					     hdset_reg_ref_t *buf);
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5LR
+ *
+ * \brief Copies data from the specified dataset to a new location and 
+ *        creates a reference to it.
+ *
+ * \param[in] obj_id        Identifier of any object in a file an 
+ *                          HDF5 reference belongs to
+ * \param[in] ref           Reference to the datasets region
+ * \param[in] file          Name of the destination file 
+ * \param[in] path          Full path to the destination dataset
+ * \param[in] block_coord   Hyperslab coordinates in the destination 
+ *                          dataset
+ * \param[out] ref_new      Region reference to the new location of 
+ *                          data
+ *
+ * \return \herr_t
+ *
+ * \details Given a data set pointed to by a region reference, the function 
+ *          H5LRcopy_reference() will copy the hyperslab data referenced by 
+ *          a datasets region reference into existing dataset specified by 
+ *          its path \p path in the file with the name \p file, and to location 
+ *          specified by the hyperslab coordinates \p block_coord. It will 
+ *          create the region reference \p ref_new to point to the new location. 
+ *          The number of elements in the old and newly specified regions has 
+ *          to be the same.
+ *
+ *          Buffer \p block_coord has size 2*rank and is the coordinates of 
+ *          the starting point following by the coordinates of the ending 
+ *          point of the hyperslab. For example, to extract a rectangular 
+ *          hyperslab region starting at element (2,2) to element (5,4) 
+ *          then \p block_coord would be {2, 2, 5, 4}.
+ *
+ * \version 1.1 Fortran wrapper introduced in this release.
+ *
+ * \since 1.0
+ *
+ */
+H5_HLRDLL herr_t H5LRcopy_reference(hid_t obj_id, hdset_reg_ref_t *ref, const char *file,
+				    const char *path, const hsize_t *block_coord, 
+				    hdset_reg_ref_t *ref_new);
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5LR
+ *
+ * \brief Copies data from a referenced region to a region in a 
+ *        destination dataset.
+ *
+ * \param[in] obj_id        Identifier of any object in a file 
+ *                          dataset region reference belongs to
+ * \param[in] ref           Dataset region reference
+ * \param[in] file          Name of the destination file 
+ * \param[in] path          Full path to the destination dataset
+ * \param[in] block_coord   Hyperslab coordinates in the destination 
+ *                          dataset
+ *
+ * \return \herr_t
+ *
+ * \details Given a dataset region reference \p ref in a source file 
+ *          specified by an identifier of any object in that file 
+ *          \p obj_id, the function will write data to the existing 
+ *          dataset \p path in file \p file to the simple hyperslab 
+ *          specified by \p block_coord.
+ *
+ *          Buffer \p block_coord has size 2*rank and is the coordinates 
+ *          of the starting point following by the coordinates of the 
+ *          ending point of the hyperslab. For example, to specify a 
+ *          rectangular hyperslab destination region starting at element 
+ *          (2,2) to element (5,4) then \p block_coord would be {2, 2, 5, 4}.
+ *
+ *          If \p path does not exist in the destination file (as may be 
+ *          the case when writing to a new file) then the dataset will be 
+ *          copied directly to the \p path and \p block_coord will be 
+ *          disregarded.
+ *
+ * \version 1.1 Fortran wrapper introduced in this release.
+ *
+ * \since 1.0
+ *
+ */
+H5_HLRDLL herr_t H5LRcopy_region(hid_t obj_id,
+				hdset_reg_ref_t *ref,
+				const char *file,
+				const char *path,
+				const hsize_t *block_coord);
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5LR
+ *
+ * \brief Creates a dataset with the region references to the data 
+ *        in all datasets located under a specified group in a file 
+ *        or creates a dataset with object references to all objects 
+ *        (groups or datasets) located under a specified group in a file.
+ *
+ * \fg_loc_id
+ * \param[in] group_path    Absolute or relative path to the group 
+ *                          at which traversal starts
+ * \param[in] ds_path       Absolute or relative path to the dataset 
+ *                          with region references to be created
+ * \param[in] index_type    Index_type; 
+ *                          see valid values below in description
+ * \param[in] order         Order in which index is traversed; 
+ *                          see valid values below in description
+ * \param[in] ref_type      Reference type;
+ *                          see valid values below in description
+ *
+ * \return \herr_t
+ *
+ * \details H5LRcreate_ref_to_all() creates a dataset with the 
+ *          region references to the data in all datasets located 
+ *          under a specified group in a file or creates a dataset with 
+ *          object references to all objects (groups or datasets) located 
+ *          under a specified group in a file.
+ *
+ *          Given a dataset path \p ds_path in a file specified by the 
+ *          \p loc_id identifier, the function H5LRcreate_ref_to_all() 
+ *          will create a contiguous one-dimensional dataset with the 
+ *          region references or object references depending on the value 
+ *          of the \p ref_type parameter. When \p ref_type is 
+ *          #H5R_DATASET_REGION, each region reference points to all data 
+ *          in a dataset encountered by an internally called H5Lvisit() 
+ *          routine, which starts at the group specified by the \p loc_id 
+ *          and \p group_path parameters. In a like manner, when
+ *          \p ref_type is #H5R_OBJECT, each object reference points to 
+ *          an object (a group or a dataset) encountered by H5Lvisit().
+ *
+ *          If \p ds_path does not exist in \p loc_id then the function 
+ *          will create the path specified by \p ds_path automatically.
+ *
+ *          \p index_type specifies the index to be used. 
+ *          Valid values include the following:
+ *          - #H5_INDEX_NAME        Alphanumeric index on name
+ *          - #H5_INDEX_CRT_ORDER   Index on creation order
+ *          .
+ *
+ *          \p order specifies the order in which objects are to be 
+ *          inspected along the index specified in \p index_type. 
+ *          Valid values include the following:
+ *          - #H5_ITER_INC      Increasing order
+ *          - #H5_ITER_DEC      Decreasing order
+ *          - #H5_ITER_NATIVE   Fastest available order
+ *          .
+ *
+ *          For more detailed information on these two parameters, 
+ *          see H5Lvisit().
+ *
+ *          \p ref_type specifies the type of the reference to be used. 
+ *          Valid values include the following:
+ *          - #H5R_DATASET_REGION   Dataset region reference
+ *          - #H5R_OBJECT           Object reference
+ *          .
+ *
+ * \version 1.1 Fortran wrapper introduced in this release.
+ *
+ * \since 1.0
+ *
+ */
+H5_HLRDLL herr_t H5LRcreate_ref_to_all(hid_t loc_id, const char *group_path,
+					 const char *ds_path, H5_index_t index_type, H5_iter_order_t order, H5R_type_t ref_type);
+
+/*-------------------------------------------------------------------------
+ *
+ * Read dataset functions
+ *
+ *-------------------------------------------------------------------------
+ */
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5LR
+ *
+ * \brief Retrieves raw data pointed to by a region reference 
+ *        to an application buffer.
+ *
+ * \param[in] obj_id        File identifier for the HDF5 file containing
+ *                          the dataset with the referenced region or an
+ *                          object identifier for any object in that file
+ * \param[in] ref           Region reference specifying data to be read
+ *                          in
+ * \param[in] mem_type      Memory datatype of data read from referenced 
+ *                          region into the application buffer
+ * \param[in,out] numelem   Number of elements to be read into buffer 
+ *                          \p buf
+ * \param[out] buf          Buffer in which data is returned to the 
+ *                          application
+ *
+ * \return \herr_t
+ *
+ * \details H5LRread_region() reads data pointed to by the region 
+ *          reference \p ref into the buffer \p buf.
+ *
+ *          \p numelem specifies the number of elements to be read 
+ *          into \p buf. When the size of the reference region is unknown, 
+ *          H5LRread_region() can be called with \p buf set to NULL; 
+ *          the number of elements in the referenced region will be returned 
+ *          in \p numelem.
+ *
+ *          The buffer buf must be big enough to hold \p numelem elements 
+ *          of type \p mem_type. For example, if data is read from the referenced 
+ *          region into an integer buffer, \p mem_type should be #H5T_NATIVE_INT 
+ *          and the buffer must be at least \c sizeof(int) * \p numelem  bytes 
+ *          in size. This buffer must be allocated by the application.
+ *
+ * \version 1.1 Fortran wrapper introduced in this release.
+ *
+ * \since 1.0
+ *
+ */
+H5_HLRDLL herr_t H5LRread_region(hid_t obj_id,
+				const hdset_reg_ref_t *ref, 
+				hid_t mem_type,
+				size_t *numelem,
+				void *buf );
+
+/*-------------------------------------------------------------------------
+ *
+ * Query dataset functions
+ *
+ *-------------------------------------------------------------------------
+ */
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5LR
+ *
+ * \brief Retrieves information about the data a region reference 
+ *        points to.
+ *
+ * \param[in] obj_id        Identifier of any object in an HDF5 file 
+ *                          the region reference belongs to.
+ * \param[in] ref           Region reference to query
+ * \param[in,out] len       Size of the buffer to store \p path in. 
+ *                          NOTE: if \p *path is not NULL then \p *len 
+ *                          must be the appropriate length
+ * \param[out] path         Full path that a region reference points to
+ * \param[out] rank         The number of dimensions of the dataset
+ *                          dimensions of the dataset pointed by 
+ *                          region reference.
+ * \param[out] dtype        Datatype of the dataset pointed by the 
+ *                          region reference.
+ * \param[out] sel_type     Type of the selection (point or hyperslab)
+ * \param[in,out] numelem   Number of coordinate blocks or 
+ *                          selected elements.
+ * \param[out] buf          Buffer containing description of the region 
+ *                          pointed by region reference
+ *
+ * \return \herr_t
+ *
+ * \details H5LRget_region_info() queries information about the data 
+ *          pointed by a region reference \p ref. It returns one of the 
+ *          absolute paths to a dataset, length of the path, dataset’s rank 
+ *          and datatype, description of the referenced region and type of 
+ *          the referenced region. Any output argument can be NULL if that 
+ *          argument does not need to be returned.
+ *
+ *          The parameter \p obj_id is an identifier for any object in the 
+ *          HDF5 file containing the referenced object. For example, it can 
+ *          be an identifier of a dataset the region reference belongs to 
+ *          or an identifier of an HDF5 file the dataset with region references 
+ *          is stored in.
+ *
+ *          The parameter \p ref is a region reference to query.
+ *
+ *          The parameter \p path is a pointer to application allocated
+ *          buffer of size \p len+1 to return an absolute path to a dataset
+ *          the region reference points to.
+ *
+ *          The parameter \p len is a length of absolute path string plus 
+ *          the \0 string terminator. If path parameter is NULL, actual 
+ *          length of the path (+1 for \0 string terminator) is returned to 
+ *          application and can be used to allocate buffer path of an 
+ *          appropriate length \p len.
+ *
+ *          The parameter \p sel_type describes the type of the selected
+ *          region. Possible values can be #H5S_SEL_POINTS for point 
+ *          selection and #H5S_SEL_HYPERSLABS for hyperslab selection.
+ *
+ *          The parameter \p numelem describes how many elements will be 
+ *          placed in the buffer \p buf. The number should be interpreted 
+ *          using the value of \p sel_type.
+ *
+ *          If value of \p sel_type is #H5S_SEL_HYPERSLABS, the parameter 
+ *          \p buf contains \p numelem blocks of the coordinates for each 
+ *          simple hyperslab of the referenced region. Each block has 
+ *          length \c 2*\p rank and is organized as follows: <"start" coordinate>, 
+ *          immediately followed by <"opposite" corner coordinate>. 
+ *          The total size of the buffer to hold the description of the 
+ *          region will be \c 2*\p rank*\p numelem. If region reference 
+ *          points to a contiguous sub-array, then the value of \p numelem 
+ *          is 1 and the block contains coordinates of the upper left and 
+ *          lower right corners of the sub-array (or simple hyperslab).
+ *
+ *          If value of \p sel_type is #H5S_SEL_POINTS, the parameter \p buf 
+ *          contains \p numelem blocks of the coordinates for each selected 
+ *          point of the referenced region. Each block has length \p rank 
+ *          and contains coordinates of the element. The total size of the 
+ *          buffer to hold the description of the region will be 
+ *          \p rank* \p numelem.
+ *
+ *
+ * \version 1.1 Fortran wrapper introduced in this release.
+ *
+ * \since 1.0
+ *
+ */
+H5_HLRDLL herr_t H5LRget_region_info(hid_t obj_id,
+				    const hdset_reg_ref_t *ref,  
+				    size_t *len, 
+				    char *path,
+				    int *rank,
+				    hid_t *dtype,
+				    H5S_sel_type *sel_type,
+				    size_t *numelem,
+				    hsize_t *buf );
+
+
+
+/*-------------------------------------------------------------------------
+ *
+ * Make dataset functions
+ *
+ *-------------------------------------------------------------------------
+ */
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5LR
+ *
+ * \brief Copies data from a specified region in a source dataset 
+ *        to a specified region in a destination dataset
+ *
+ * \param[in] file_src          Name of the source file
+ * \param[in] path_src          Full path to the source dataset
+ * \param[in] block_coord_src   Hyperslab coordinates in the 
+ *                              source dataset
+ * \param[in] file_dest         Name of the destination file
+ * \param[in] path_dest         Full path to the destination dataset
+ * \param[in] block_coord_dset  Hyperslab coordinates in the 
+ *                              destination dataset
+ *
+ * \return \herr_t
+ *
+ * \details Given a path to a dataset \p path_src in a file with the 
+ *          name \p file_src, and description of a simple hyperslab of 
+ *          the source \p block_coord_src, the function will write data 
+ *          to the dataset \p path_dest in file \p file_dest to the 
+ *          simple hyperslab specified by \p block_coord_dset. 
+ *          The arrays \p block_coord_src and \p block_coord_dset have 
+ *          a length of 2*rank and are the coordinates of the starting 
+ *          point following by the coordinates of the ending point of the 
+ *          hyperslab. For example, to specify a rectangular hyperslab 
+ *          destination region starting at element (2,2) to element (5,4) 
+ *          then \p block_coord_dset would be {2, 2, 5, 4}.
+ *
+ *          If \p path_dest does not exist in the destination file 
+ *          (as may be the case when writing to a new file) then the 
+ *          dataset will be copied directly to the \p path_dest and 
+ *          \p block_coord_dset will be disregarded.
+ *
+ * \version 1.1 Fortran wrapper introduced in this release.
+ *
+ * \since 1.0
+ *
+ */
+H5_HLRDLL herr_t H5LTcopy_region(const char *file_src,
+				const char *path_src,
+				const hsize_t *block_coord_src,
+				const char *file_dest,
+				const char *path_dest,
+				const hsize_t *block_coord_dset);
+
+/*-------------------------------------------------------------------------
+ *
+ * Read dataset functions
+ *
+ *-------------------------------------------------------------------------
+ */
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5LR
+ *
+ * \brief Reads selected data to an application buffer.
+ *
+ * \param[in] file          Name of file
+ * \param[in] path          Full path to a dataset
+ * \param[in] block_coord   Hyperslab coordinates
+ * \param[in] mem_type      Memory datatype, describing the buffer 
+ *                          the referenced data will be read into
+ * \param[out] buf          Buffer containing data from the 
+ *                          referenced region
+ *
+ * \return \herr_t
+ *
+ * \details H5LTread_region() reads data from a region described by 
+ *          the hyperslab coordinates in \p block_coord, located in 
+ *          the dataset specified by its absolute path \p path in a 
+ *          file specified by its name \p file. Data is read into a 
+ *          buffer \p buf of the datatype that corresponds to the 
+ *          HDF5 datatype specified by \p mem_type.
+ *
+ *          Buffer \p block_coord has size 2*rank and is the coordinates 
+ *          of the starting point following by the coordinates of the 
+ *          ending point of the hyperslab. For example, to extract a 
+ *          rectangular hyperslab region starting at element (2,2) to 
+ *          element (5,4) then \p block_coord would be {2, 2, 5, 4}.
+ *
+ *          Buffer \p buf should be big enough to hold selected elements 
+ *          of the type that corresponds to the \p mem_type
+ *
+ * \version 1.1 Fortran wrapper introduced in this release.
+ *
+ * \since 1.0
+ *
+ */
+H5_HLRDLL herr_t  H5LTread_region(const char *file,
+				 const char *path,
+				 const hsize_t *block_coord,
+				 hid_t mem_type,
+				 void *buf );
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5LR
+ *
+ * \brief Retrieves the values of quality flags for each element 
+ *        to the application provided buffer.
+ *
+ * \param[in] dset_id   Identifier of the dataset with bit-field values
+ * \param[in] num_values    Number of the values to be extracted
+ * \param[in] offset        Array of staring bits to be extracted from 
+ *                          the element; valid values: 0 (zero) through 7
+ * \param[in] lengths       Array of the number of bits to be extracted 
+ *                          for each value
+ * \param[in] space         Dataspace identifier, describing the elements 
+ *                          to be read from the dataset with bit-field 
+ *                          values
+ * \param[out] buf          Buffer to read the values in
+ *
+ * \return \herr_t
+ *
+ * \details H5LTread_bitfield_value() reads selected elements from a 
+ *          dataset specified by its identifier \p dset_id, and unpacks 
+ *          the bit-field values to a buffer \p buf.
+ *
+ *          The parameter \p space is a space identifier that indicates 
+ *          which elements of the dataset should be read.
+ *
+ *          The parameter \p offset is an array of length \p num_values; 
+ *          the i<sup>th</sup> element of the array holds the value of the
+ *          starting bit of the i<sup>th</sup> bit-field value. 
+ *          Valid values are: 0 (zero) through 7.
+ *
+ *          The parameter \p lengths is an array of length \p num_values; 
+ *          the i<sup>th</sup> element of the array holds the number of 
+ *          bits to be extracted for the i<sup>th</sup> bit-field value. 
+ *          Extracted bits will be interpreted as a base-2 integer value. 
+ *          Each value will be converted to the base-10 integer value and 
+ *          stored in the application buffer. 
+ *
+ *          Buffer \p buf is allocated by the application and should be big 
+ *          enough to hold \c num_sel_elem * \p num_values elements of the 
+ *          specified type, where \c num_sel_elem is a number of the elements 
+ *          to be read from the dataset. Data in the buffer is organized 
+ *          as \p num_values values for the first element, followed by the 
+ *          \p num_values values for the second element, ... , followed by 
+ *          the \p num_values values for the 
+ *          \c num_selected_elem<sup>th</sup> element.
+ *
+ * \version 1.1 Fortran wrapper introduced in this release.
+ *
+ * \since 1.0
+ *
+ */
+H5_HLRDLL herr_t H5LTread_bitfield_value(hid_t dset_id, int num_values, const unsigned *offset,
+					const unsigned *lengths, hid_t space, int *buf);
+
diff --git a/doxygen/dox/high_level/high_level.dox b/doxygen/dox/high_level/high_level.dox
new file mode 100644
index 0000000..c53d298
--- /dev/null
+++ b/doxygen/dox/high_level/high_level.dox
@@ -0,0 +1,29 @@
+/** \page high_level High-level library
+ * The high-level HDF5 library includes several sets of convenience and standard-use APIs to 
+ * facilitate common HDF5 operations.
+ *
+ * <ul>
+ * <li>\ref H5LT "Lite (H5LT, H5LD)"
+ * \n
+ * Functions to simplify creating and manipulating datasets, attributes and other features
+ * <li>\ref H5IM "Image (H5IM)"
+ * \n
+ * Creating and manipulating HDF5 datasets intended to be interpreted as images
+ * <li>\ref H5TB "Table (H5TB)"
+ * \n
+ * Creating and manipulating HDF5 datasets intended to be interpreted as tables
+ * <li>\ref H5PT "Packet Table (H5PT)"
+ * \n
+ * Creating and manipulating HDF5 datasets to support append- and read-only operations on table data
+ * <li>\ref H5DS "Dimension Scale (H5DS)"
+ * \n
+ * Creating and manipulating HDF5 datasets that are associated with the dimension of another HDF5 dataset
+ * <li>\ref H5DO "Optimizations (H5DO)"
+ * \n
+ * Bypassing default HDF5 behavior in order to optimize for specific use cases
+ * <li>\ref H5LR "Extensions (H5LR, H5LT)"
+ * \n
+ * Working with region references, hyperslab selections, and bit-fields
+ * </ul>
+ * 
+ */
diff --git a/doxygen/examples/H5DO_examples.c b/doxygen/examples/H5DO_examples.c
new file mode 100644
index 0000000..7a33c6b
--- /dev/null
+++ b/doxygen/examples/H5DO_examples.c
@@ -0,0 +1,220 @@
+/* -*- c-file-style: "stroustrup" -*- */
+
+//! <!-- [H5DOwrite] -->
+
+#include <zlib.h>
+#include <math.h>
+#define DEFLATE_SIZE_ADJUST(s) (ceil(((double)(s)) * 1.001) + 12)
+                :
+                :
+size_t       buf_size = CHUNK_NX*CHUNK_NY*sizeof(int);
+                const Bytef *z_src = (const Bytef *)(direct_buf);
+                Bytef *      z_dst; /* Destination buffer            */
+                uLongf       z_dst_nbytes = (uLongf)DEFLATE_SIZE_ADJUST(buf_size);
+                uLong        z_src_nbytes = (uLong)buf_size;
+                int          aggression   = 9; /* Compression aggression setting */
+                uint32_t     filter_mask  = 0;
+                size_t       buf_size     = CHUNK_NX * CHUNK_NY * sizeof(int);
+
+                /* Create the data space */
+                if ((dataspace = H5Screate_simple(RANK, dims, maxdims)) < 0)
+                    goto error;
+
+                /* Create a new file */
+                if ((file = H5Fcreate(FILE_NAME5, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT)) < 0)
+                    goto error;
+
+                /* Modify dataset creation properties, i.e. enable chunking and compression */
+                if ((cparms = H5Pcreate(H5P_DATASET_CREATE)) < 0)
+                    goto error;
+
+                if ((status = H5Pset_chunk(cparms, RANK, chunk_dims)) < 0)
+                    goto error;
+
+                if ((status = H5Pset_deflate(cparms, aggression)) < 0)
+                    goto error;
+
+                /* Create a new dataset within the file using cparms creation properties */
+                if ((dset_id = H5Dcreate2(file, DATASETNAME, H5T_NATIVE_INT, dataspace, H5P_DEFAULT, cparms,
+                                          H5P_DEFAULT)) < 0)
+                    goto error;
+
+                /* Initialize data for one chunk */
+                for (i = n = 0; i < CHUNK_NX; i++)
+                    for (j = 0; j < CHUNK_NY; j++)
+                        direct_buf[i][j] = n++;
+
+                /* Allocate output (compressed) buffer */
+                outbuf = malloc(z_dst_nbytes);
+                z_dst  = (Bytef *)outbuf;
+
+                /* Perform compression from the source to the destination buffer */
+                ret = compress2(z_dst, &z_dst_nbytes, z_src, z_src_nbytes, aggression);
+
+                /* Check for various zlib errors */
+                if (Z_BUF_ERROR == ret) {
+                    fprintf(stderr, "overflow");
+                    goto error;
+                }
+                else if (Z_MEM_ERROR == ret) {
+                    fprintf(stderr, "deflate memory error");
+                    goto error;
+                }
+                else if (Z_OK != ret) {
+                    fprintf(stderr, "other deflate error");
+                    goto error;
+                }
+
+                /* Write the compressed chunk data repeatedly to cover all the
+                 *  * chunks in the dataset, using the direct write function.     */
+                for (i = 0; i < NX / CHUNK_NX; i++) {
+                    for (j = 0; j < NY / CHUNK_NY; j++) {
+                        status =
+                            H5DOwrite_chunk(dset_id, H5P_DEFAULT, filter_mask, offset, z_dst_nbytes, outbuf);
+                        offset[1] += CHUNK_NY;
+                    }
+                    offset[0] += CHUNK_NX;
+                    offset[1] = 0;
+                }
+
+                /* Overwrite the first chunk with uncompressed data.  Set the filter mask to
+                 *  * indicate the compression filter is skipped */
+                filter_mask = 0x00000001;
+                offset[0] = offset[1] = 0;
+                if (H5DOwrite_chunk(dset_id, H5P_DEFAULT, filter_mask, offset, buf_size, direct_buf) < 0)
+                    goto error;
+
+                /* Read the entire dataset back for data verification converting ints to longs */
+                if (H5Dread(dataset, H5T_NATIVE_LONG, H5S_ALL, H5S_ALL, H5P_DEFAULT, outbuf_long) < 0)
+                    goto error;
+
+                /* Data verification here */
+            :
+            :
+
+            //! <!-- [H5DOwrite] -->
+
+            //! <!-- [H5DOread] -->
+
+#include <zlib.h>
+#include <math.h>
+#define DEFLATE_SIZE_ADJUST(s) (ceil(((double)(s)) * 1.001) + 12)
+                :
+                :
+size_t       buf_size = CHUNK_NX*CHUNK_NY*sizeof(int);
+            const Bytef *z_src = (const Bytef *)(direct_buf);
+            Bytef *      z_dst; /* Destination buffer            */
+            uLongf       z_dst_nbytes = (uLongf)DEFLATE_SIZE_ADJUST(buf_size);
+            uLong        z_src_nbytes = (uLong)buf_size;
+            int          aggression   = 9; /* Compression aggression setting */
+            uint32_t     filter_mask  = 0;
+            size_t       buf_size     = CHUNK_NX * CHUNK_NY * sizeof(int);
+            /* For H5DOread_chunk() */
+            void *       readbuf = NULL;                   /* Buffer for reading data */
+            const Bytef *pt_readbuf;                       /* Point to the buffer for data read */
+            hsize_t      read_chunk_nbytes;                /* Size of chunk on disk */
+            int          read_dst_buf[CHUNK_NX][CHUNK_NY]; /* Buffer to hold un-compressed data */
+
+            /* Create the data space */
+            if ((dataspace = H5Screate_simple(RANK, dims, maxdims)) < 0)
+                goto error;
+
+            /* Create a new file */
+            if ((file = H5Fcreate(FILE_NAME5, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT)) < 0)
+                goto error;
+
+            /* Modify dataset creation properties, i.e. enable chunking and compression */
+            if ((cparms = H5Pcreate(H5P_DATASET_CREATE)) < 0)
+                goto error;
+
+            if ((status = H5Pset_chunk(cparms, RANK, chunk_dims)) < 0)
+                goto error;
+
+            if ((status = H5Pset_deflate(cparms, aggression)) < 0)
+                goto error;
+
+            /* Create a new dataset within the file using cparms creation properties */
+            if ((dset_id = H5Dcreate2(file, DATASETNAME, H5T_NATIVE_INT, dataspace, H5P_DEFAULT, cparms,
+                                      H5P_DEFAULT)) < 0)
+                goto error;
+
+            /* Initialize data for one chunk */
+            for (i = n = 0; i < CHUNK_NX; i++)
+                for (j = 0; j < CHUNK_NY; j++)
+                    direct_buf[i][j] = n++;
+
+            /* Allocate output (compressed) buffer */
+            outbuf = malloc(z_dst_nbytes);
+            z_dst  = (Bytef *)outbuf;
+
+            /* Perform compression from the source to the destination buffer */
+            ret = compress2(z_dst, &z_dst_nbytes, z_src, z_src_nbytes, aggression);
+
+            /* Check for various zlib errors */
+            if (Z_BUF_ERROR == ret) {
+                fprintf(stderr, "overflow");
+                goto error;
+            }
+            else if (Z_MEM_ERROR == ret) {
+                fprintf(stderr, "deflate memory error");
+                goto error;
+            }
+            else if (Z_OK != ret) {
+                fprintf(stderr, "other deflate error");
+                goto error;
+            }
+
+            /* Write the compressed chunk data repeatedly to cover all the
+             *  * chunks in the dataset, using the direct write function.     */
+            for (i = 0; i < NX / CHUNK_NX; i++) {
+                for (j = 0; j < NY / CHUNK_NY; j++) {
+                    status = H5DOwrite_chunk(dset_id, H5P_DEFAULT, filter_mask, offset, z_dst_nbytes, outbuf);
+                    offset[1] += CHUNK_NY;
+                }
+                offset[0] += CHUNK_NX;
+                offset[1] = 0;
+            }
+
+            if (H5Fflush(dataset, H5F_SCOPE_LOCAL) < 0)
+                goto error;
+
+            if (H5Dclose(dataset) < 0)
+                goto error;
+
+            if ((dataset = H5Dopen2(file, DATASETNAME1, H5P_DEFAULT)) < 0)
+                goto error;
+
+            offset[0] = CHUNK_NX;
+            offset[1] = CHUNK_NY;
+
+            /* Get the size of the compressed chunk */
+            ret = H5Dget_chunk_storage_size(dataset, offset, &read_chunk_nbytes);
+
+            readbuf    = HDmalloc(read_chunk_nbytes);
+            pt_readbuf = (const Bytef *)readbuf;
+
+            /* Use H5DOread_chunk() to read the chunk back */
+            if ((status = H5DOread_chunk(dataset, H5P_DEFAULT, offset, &read_filter_mask, readbuf)) < 0)
+                goto error;
+
+            ret =
+                uncompress((Bytef *)read_dst_buf, (uLongf *)&buf_size, pt_readbuf, (uLong)read_chunk_nbytes);
+
+            /* Check for various zlib errors */
+            if (Z_BUF_ERROR == ret) {
+                fprintf(stderr, "error: not enough room in output buffer");
+                goto error;
+            }
+            else if (Z_MEM_ERROR == ret) {
+                fprintf(stderr, "error: not enough memory");
+                goto error;
+            }
+            else if (Z_OK != ret) {
+                fprintf(stderr, "error: corrupted input data");
+                goto error;
+            }
+
+            /* Data verification here */
+            :
+            :
+//! <!-- [H5DOread] -->
diff --git a/doxygen/examples/H5LDget_dset_elmts.c b/doxygen/examples/H5LDget_dset_elmts.c
new file mode 100644
index 0000000..e23299a
--- /dev/null
+++ b/doxygen/examples/H5LDget_dset_elmts.c
@@ -0,0 +1,143 @@
+/* -*- c-file-style: "stroustrup" -*- */
+
+//! <!-- [first_declare] -->
+
+DATASET "DSET1" {DATATYPE H5T_STD_I32LE DATASPACE SIMPLE{(4, 13) / (60, 100)} : : }
+
+//! <!-- [first_declare] -->
+
+//! <!-- [first_reading] -->
+
+/* open the HDF5 file */
+fid = H5Fopen(FILE, H5F_ACC_RDWR, H5P_DEFAULT);
+
+/* open the dataset */
+did = H5Dopen2(fid, "DSET1", H5P_DEFAULT);
+        :
+        :
+    /* define hsize_t dims[2]; */
+    /* define hsize_t new_dims[2]; */
+    /* get the dataset's current dimension sizes */
+    H5LDget_dset_dims(did, dims);
+
+        /* extend the dataset by 2 */
+        new_dims[0] = dims[0] + 2;
+        new_dims[1] = dims[1] + 2;
+        H5Dset_extent(did, new_dims)
+
+            /* write data to the extended dataset */
+            : :
+            /* get the size of the dataset's data type */
+            type_size = H5LDget_dset_type_size(did, NULL);
+        :
+        :
+    /* allocate buffer for storing selected data elements from the dataset */
+    /* calculate # of selected elements from dims & new_dims */
+    /* buffer size = type_size * number of selected elements */
+        :
+        :
+    /* read the selected elements from the dataset into buf */
+    H5LDget_dset_elmts(did, dims, new_dims, NULL, buf);
+        :
+        :
+    H5Dclose(did);
+        H5Fclose(fid);
+
+        //! <!-- [first_reading] -->
+
+        //! <!-- [first_output] -->
+
+    data for elements (0, 13), (0, 14) 
+    data for elements (1, 13), (1, 14) 
+    data for elements (2, 13), (2, 14) 
+    data for elements (3, 13), (3, 14)
+    data for elements (4, 0), (4, 1), (4, 2)......................(4, 13), (4, 14)
+    data for elements (5, 0), (5, 1), (5, 2)......................(5, 13), (5, 14)
+
+//! <!-- [first_output] -->
+
+
+//! <!-- [second_declare] -->
+
+    DATASET "DSET2" {
+    DATATYPE  H5T_COMPOUND {
+        H5T_STD_I32LE "a";
+    H5T_STD_I32LE "b";
+    H5T_ARRAY
+    {
+        [4] H5T_STD_I32LE
+    }
+    "c";
+    H5T_STD_I32LE "d";
+    H5T_STD_I32LE "e";
+    H5T_COMPOUND
+    {
+        H5T_STD_I32LE "a";
+        H5T_STD_I32LE "b";
+        H5T_ARRAY
+        {
+            [4] H5T_STD_I32LE
+        }
+        "c";
+        H5T_STD_I32LE "d";
+        H5T_STD_I32LE "e";
+    }
+    "s2";
+    }
+    DATASPACE SIMPLE
+    {
+        (5) / (5)
+    }
+    ::
+    }
+
+    //! <!-- [second_declare] -->
+
+    //! <!-- [second_reading] -->
+
+    /* open the HDF5 file */
+    fid = H5Fopen(FILE, H5F_ACC_RDWR, H5P_DEFAULT);
+
+    /* open the dataset */
+    did = H5Dopen2(fid, "DSET2", H5P_DEFAULT);
+
+    /* define hsize_t dims[1]; */
+    /* define hsize_t new_dims[1]; */
+        :
+        :
+    /* get the dataset's current dimension size */
+    H5LDget_dset_dims(did, dims);
+
+        /* extend the dataset by 2 */
+        new_dims[0] = dims[0] + 2;
+        H5Dset_extent(did, new_dims);
+        :
+        :
+    /* write data to the extended part of the dataset */
+        :
+        :
+    /* #define fields "d,s2.c" */
+    /* get the size of the dataset's data type for the selected fields */
+    type_size = H5LDget_dset_type_size(did, fields);
+        :
+        :
+    /* allocate buffer for storing selected data elements from the dataset */
+    /* calculate # of selected elements from dims & new_dims */
+    /* buffer size = type_size * number of selected elements */
+        :        
+        :
+    /* read the selected elements from the dataset into buf */
+    H5LD_get_dset_elmts(did, dims, new_dims, fields, buf);
+        :
+        :
+    H5Dclose(did);
+        H5Fclose(fid);
+
+        //! <!-- [second_reading] -->
+
+        //! <!-- [second_output] -->
+
+    Data for element (5): integer value for "d", 4 integer values for array "s2.c"
+    Data for element (6): integer value for "d", 4 integer values for array "s2.c"
+
+//! <!-- [second_output] -->
diff --git a/doxygen/examples/H5LT_examples.c b/doxygen/examples/H5LT_examples.c
new file mode 100644
index 0000000..5ed4c29
--- /dev/null
+++ b/doxygen/examples/H5LT_examples.c
@@ -0,0 +1,27 @@
+/* -*- c-file-style: "stroustrup" -*- */
+
+//! <!-- [get_attribute_info] -->
+
+H5T_class_t type_class;
+size_t      type_size;
+hsize_t     dims[0];
+... status = H5LTget_attribute_info(file_id, "/", STRNAME, dims, &type_class, &type_size);
+if (type_class == H5T_STRING) {
+    printf("Attribute is a string.\n");
+    printf("String size: %i\n", type_size);
+
+    //! <!-- [get_attribute_info] -->
+
+    //! <!-- [enum] -->
+
+    “H5T_ENUM
+    {
+        H5T_NATIVE_INT;
+        “Bob” 0;
+        “Elena” 1;
+        “Quincey” 2;
+        “Frank” 3;
+    }
+    ”
+
+//! <!-- [enum] -->
diff --git a/doxygen/examples/H5TBAget_fill.c b/doxygen/examples/H5TBAget_fill.c
new file mode 100644
index 0000000..15eae8b
--- /dev/null
+++ b/doxygen/examples/H5TBAget_fill.c
@@ -0,0 +1,43 @@
+unsigned char tmp_fill_buf[40];
+...
+
+    file_id = H5Fopen(FILENAME, H5F_ACC_RDWR, H5P_DEFAULT);
+dataset_id  = H5Dopen(file_id, TABLE_NAME, H5P_DEFAULT);
+datatype_id = H5Dget_type(dataset_id);
+
+status = H5TBget_table_info(file_id, TABLE_NAME, &nfields, &nrecords);
+
+hasfill = H5TBAget_fill(file_id, TABLE_NAME, dataset_id, tmp_fill_buf);
+
+for (i = 0; i < nfields; i++) {
+    member_type_id     = H5Tget_member_type(datatype_id, (unsigned)i);
+    native_mem_type_id = H5Tget_native_type(member_type_id, H5T_DIR_ASCEND);
+    member_offset      = H5Tget_member_offset(datatype_id, (unsigned)i);
+    printf("member_offset: %i\n", member_offset);
+    memb_class = H5Tget_class(member_type_id);
+    switch (memb_class) {
+        case H5T_INTEGER:
+            /* convert unsigned char array to integer */
+            break;
+        case H5T_FLOAT:
+            /* convert unsigned char array to double or float */
+
+            if (H5Tequal(native_mem_type_id, H5T_NATIVE_DOUBLE)) {
+            }
+            else if (H5Tequal(native_mem_type_id, H5T_NATIVE_FLOAT)) {
+                f.i = tmp_fill_buf[member_offset] | (tmp_fill_buf[member_offset + 1] << 8) |
+                      (tmp_fill_buf[member_offset + 2] << 16) | (tmp_fill_buf[member_offset + 3] << 24);
+                printf("Field %i  Fill Value:  %lf\n", i, f.f);
+            }
+            break;
+
+        case H5T_STRING:
+            /* convert unsigned char array to string */
+            strsize = H5Tget_size(member_type_id);
+
+            printf("Field %i  Fill Value: ", i);
+            for (j = 0; j < strsize; j++)
+                printf("%c", tmp_fill_buf[member_offset + j]);
+            printf("\n");
+            break;
+    }